No issues have stirred the peaceable waters of zoology more violently these past 200 years than those of systematics: which animals are related to which. The trouble is that animals that look alike often have different ancestry - as with dolphins and fish, which merely provide an example of 'convergent evolution'. But sometimes animals that look different have both descended from a common ancestor - as seems to be true of condors and storks, even though condors look like ordinary vultures.

Many such matters remained unresolved (and controversial) until, in the Seventies, molecular biologists swept in like the US cavalry and showed that relationships could be revealed unequivocally by studying the chemistry of genes. It seemed necessary merely to compare the structure of the DNA. Such studies showed that humans are almost the same genetically as chimpanzees, and that the two probably diverged no more than 8 million years ago.

But zoology would be boring if it was that easy. That the DNA studies themselves require all-too-human judgement has long been suspected, and is now made clear through creatures that have puzzled systematists since the 18th century: bats, and their relationship to Primates - that is, to lemurs, tarsiers, monkeys, apes and ourselves. John Pettigrew of the University of Queensland argues that fruit bats, which include 'flying foxes', effectively are Primates and are not related to 'ordinary' bats at all. To be sure, fruit-bat DNA seems very like the DNA of, say, pipistrelles, and nothing like that of monkeys. But, says Dr Pettigrew, DNA itself is subject to the vagaries of evolution, and in this instance, as perhaps in many others, the DNA is lying.

Zoologists generally place bats as a whole into the 'order' Chiroptera - but they divide that group into two sub-orders. First come the Megachiroptera, or 'megabats', which include 162 species of fruit bat including the huge 'flying foxes' with a wingspan of a metre or more. Then there are the Microchiroptera, or 'microbats', with 815 species of pipistrelles, Daubenton's, horseshoes and the rest. There is a general difference in size between the groups (though much overlap) but the similarities are obvious.

Dr Pettigrew, however, points to at least 50 differences. Microbats, for example, use echo location for hunting but megabats do not - or if they do, employ a different, cruder system. The fossil record shows that microbats evolved before megabats, so if the two are related

then megas must have arisen from micros. But, if so, why did megabats lose echo location, which would have been useful for them since they, too, forage at night? And why, having abandoned echo location, did some megabats re-evolve their own system?

Instead, Dr Pettigrew points to the similarities between megabats and yet another order of mammals, the Dermopterans, otherwise known as colugos. These are gliders from South-east Asia and look so like Primates that they are often called 'flying lemurs'. Indeed, Linnaeus argued in the 18th century that colugos were Primates, while modern zoologists generally agree that Dermoptera and Primates are closely related. Indeed, the fossils suggest that colugos descended from Primates.

In practice, some of Dr Pettigrew's suggested resemblances between megabats and colugos, such as the wing structure, could be due to convergence. But others seem to reflect a relationship - including many details of brain anatomy, such as the way in which particular groups of cells are packed. Such obscure features are not readily affected by pressures of the environment and are usually ascribed to common ancestry.

There is one anatomical complication. Some zoologists point out that colugos have such small brains that they could not be related either to Primates or megabats. But, says Dr Pettigrew, this is because colugos eat the leaves of tropical trees. Such leaves are high in toxins and committed eaters of tropical tree leaves tend to have small brains for this reason alone, irrespective of ancestry. Koalas and hoatzins (primitive South American birds) have similarly pea-sized brains. Never mind the size, says Dr Pettigrew, look at the structure.

In fact, he says, megabats are probably descended from ancient colugos, since colugos are more primitive and have an older fossil record. But if megabats are descended from colugos, and colugos from Primates, then megabats in effect are Primates. Microbats, on the other hand, as most zoologists agree, had insectivore ancestors.

Dr Pettigrew's theory gained ground in the mid-Eighties - until the molecular biologists came on the scene. They showed that megabat DNA and microbat DNA were very similar. And both were distinct from that of Primates.

But, says Dr Pettigrew, the resemblance of megabat and microbat DNA is itself due to convergence. DNA is compounded from four bases: adenine, thymine, guanine, and cytosine (A, T, G, and C). Megabat and microbat DNA are both rich in A (and therefore T, which always accompanies A). Why should this be, if common ancestry is not the cause? Well, A, adenine, is very like adenosine. Adenosine is the basis of the molecule ATP. ATP provides cells with energy. So animals tend to have a high concentration of ATP if they have a high metabolic rate and therefore a high demand for instant energy.

Now the twist. DNA - which is always being copied and otherwise abused - is in constant need of repair. Second, only a small proportion of the total DNA molecule functions as genes, the rest seems almost functionless. Repairs to the functional bits have to be accurate but repairs to the rest - the majority - can be more rough and ready. In the cells of animals with a high metabolic rate, there are huge amounts of adenosine, so this base, albeit slightly modified, is used for DNA repair. Thus animals with a high metabolic rate have DNA that is rich in A (and therefore inevitably in T). All bats, as flying animals, have a high metabolic rate, and thus their DNA is rich in A and T. So, too, do shrews and honey- bees - which also have a high metabolic rate. But, says Dr Pettigrew, if you take away the A-T bias, which is brought about by the high rate of metabolism, you find that megabat DNA is more like that of Primates and colugos than that of microbats.

Further studies - for example on the DNA of more animals of high and low metabolic rates - must explore Dr Pettigrew's arguments. For my part, I feel he is right: that mammals produced not one, but two distinct groups of powered fliers. In any case, his general argument is salutary. DNA does not provide the royal road to unequivocal insight. Systematists must use their judgement in assessing DNA, just as they do when looking at any other feature - behaviour, brain structure or bones.

Colin Tudge's latest book, 'Engineer in the Garden', on modern genetics, is published by Jonathan Cape, pounds 17.99.